I have a DNA file like below and I am able to write a short program which finds/not an input motif, but I dont understand how I can include in the code to report which position the motif was found. Example I want to find the first or all "GAT" motifs and want the program to report which position (beginning to end) of the dna motif was found. So in this example GAT (in bold should report 10-12) and if found more than once the other positions too. Can someone explain how to report matching position on strings ??
Hi,
I need to insert strings "0000 00" at the each line within the file.
The postion is 37 to 42.
ex.
name1 name2 0000 00
nam name 0000 00
The "0000 00" in two lines should be lined up.
I don't know why it's not lined up when I posted it.
Can anyone help? (14 Replies)
Hi,
I have a challenging task,in which i have to find the duplicate files by its name and size,then i need to take anyone of the file.Then i need to open the file and find for more than one pattern and count of that pattern.
Note:These are the samples of two files,but i can have more... (2 Replies)
Hi,
I have this input file called ttbitnres (which is catenated and sorted):-
8 0.4444 213
10 0.5555 342
11 0.5555 321
12 0.5555 231
13 0.4444 400
My code is at :-
#!/bin/bash
echo -e Version "\t" Number of Pass "\t" Number of Fail "\t" Rank Position "\t"Min "\t" Max... (1 Reply)
Hello,
I would like to find an efficient way to compare a pair of strings that differ at one position, and return the difference and position.
For example:
String1 123456789
String2 123454789
returning something - position 6, 6/4
Thanks in advance,
Mike (5 Replies)
Hi,
I need to search for some strings in specific positions in a file.
If the strings: "foo1", "foo2" or "foo3" is on position 266 or position 288 in a file i want the whole line printed.
Any idea how to do it? (5 Replies)
HI All,
am trying to find the position of space in a variable, it is working for other characters other than space
ulab="ulab1|ulab2"
find_pos=`expr index $ulab '|'`
echo $find_pos
above code worked fine but below one says syntax error
ulab="ulab ulab2"
find_pos=`expr index $ulab ' '`... (2 Replies)
i have a requirement like this
if the line contains from position 294 to 299 is equal to "prabhu" ,then print entire line .
i want to use awk
awk '{if(substr(294-299) == 'prabhu') print "line" }' filename (1 Reply)
I am not an expert with linux, but following various posts on this forum, I have been trying to write a script to match pattern of charters occurring together in a file.
My file has approximately 200 million characters (upper and lower case), with about 50 characters per line. I have merged all... (5 Replies)
I am using bash in Fedora 30
From the below lines (ls -l output), how can I print whatever is between the strings 'status_' and '.log'
$ ls -l | grep -i status
-rw-rw-r--. 1 sysadmin sysadmin 378530 Nov 11 21:58 status_vsbm1.log
-rw-rw-r--. 1 sysadmin sysadmin 428776 Nov 11 21:58... (8 Replies)
Discussion started by: kraljic
8 Replies
LEARN ABOUT DEBIAN
bio::tools::analysis::dna::esefinder
Bio::Tools::Analysis::DNA::ESEfinder(3pm) User Contributed Perl Documentation Bio::Tools::Analysis::DNA::ESEfinder(3pm)NAME
Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server
SYNOPSIS
use Bio::Tools::Analysis::DNA::ESEfinder;
use strict;
my $seq; # a Bio::PrimarySeqI or Bio::SeqI object
$seq = Bio::Seq->new(
-primary_id => 'test',
-seq=>'atgcatgctaggtgtgtgttttgtgggttgtactagctagtgat'.
-alphabet=>'dna');
my $ese_finder = Bio::Tools::Analysis::DNA::ESEfinder->
new(-seq => $seq);
# run ESEfinder prediction on a DNA sequence
$ese_finder->run();
die "Could not get a result"
unless $ese_finder->status =~ /^COMPLETED/;
print $ese_finder->result; # print raw prediction to STDOUT
foreach my $feat ( $ese_finder->result('Bio::SeqFeatureI') ) {
# do something to SeqFeature
# e.g. print as GFF
print $feat->gff_string, "
";
# or store within the sequence - if it is a Bio::SeqI
$seq->add_SeqFeature($feat)
}
DESCRIPTION
This class is a wrapper around the ESEfinder web server which uses experimentally defined scoring matrices to identify possible exonic
splicing enhancers in human transcripts.
The results can be retrieved in 4 ways.
1. "$ese_finder->result('')" retrieves the raw text output of the program
2. "$ese_finder->result('all')" returns a Bio::Seq::Meta::Array object with prediction scores for all residues in the sequence
3. "$ese_finder->result('Bio::SeqFeatureI')" returns an array of Bio::SeqFeature objects for sequences with significant scores. Feature
tags are score, motif, SR_protein and method
4. "$ese_finder->result('raw')" returns an array of significant matches with each element being a reference to [SR_protein, position,
motif, score]
See <http://rulai.cshl.edu/tools/ESE2/>
This the second implentation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class
uses a web resource and therefore inherits from Bio::WebAgent.
SEE ALSO
Bio::SimpleAnalysisI, Bio::WebAgent
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
perl v5.14.2 2012-03-02 Bio::Tools::Analysis::DNA::ESEfinder(3pm)